Plotting arbitrary lines at Gviz plotTracks

Question

[yogacacarolom]

I would like to plot lines between two itens at different AnnotationTrack, or simple between two coordinates in my Gvizplot.

genes data.frame:

      start      end
     72529373 72690449
     75457896 75536848
     76867833 76922959
     75664651 75870596
     76958977 77024110
     72065147 72204484
     74198711 74199129
     74816044 74978179
     76758753 76864805
     77032585 77176916
     73574461 73704802

library(Gviz)
library(GenomicRanges)
ideoTrack <- IdeogramTrack(genome = "bosTau6", chromosome = "chr12", fontsize=14, ucscChromosomeNames=TRUE)
axisTrack <- GenomeAxisTrack(range = IRanges(start  = c(71959908, 76756891), end = c(72409907, 77206892), names = rep("Neighborhood", 2)), fontsize=14, showId = TRUE, cex.id = 0.5, col.id = "black")
aTgenes1 <- AnnotationTrack(genes, name = "Genes", genome ="bosTau6", chromosome ="chr12", showId = TRUE, stacking ="dense")
aTgenes2 <- AnnotationTrack(genes, name = "Genes", genome ="bosTau6", chromosome ="chr12", showId = TRUE, stacking ="dense")
plotTracks(list(ideoTrack, axisTrack, aTgenes1, aTgenes2), from = 71959908, to = 77206892, sizes=c(1,1,1,1), margin=40, littleTicks = TRUE)

This above code result in this plot:

Considering the 11 plotted genes (the fourth gene is very small and hard to see), I have the follow interaction between the genes:

• gene 1 -> gene 2 and gene 11
• gene 3 -> gene 5
• gene 7 -> gene 6

With this interaction I expect some final plot similar to this picture:

I had tried some approaches that work in normal plots but not to Gviz plots. Some ideas? Thank you very much!

[Devon Ryan]

I have a feeling that you'll get the best reply to this from the bioconductor mailing list. Be sure to CC: Florian Hahne, since he's the Gviz maintainer. I suggest this list since in order to programmatically draw things, you'll need to extract the coordinates to which various objects will be drawn and doing this will require a fairly high level of familiarity with the inner-workings of the package (this is something which only the maintainer is likely to have).

The maintainers might also be able to suggest another way to do this or, at the very least, give you some insight as to how doable this approach is.

[stianlagstad]

Did you get anywhere with this?